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Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

  • Tanggis Bohnuud
  • George Jones
  • Ora Schueler-FurmanEmail author
  • Dima KozakovEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1561)

Abstract

Peptide-mediated interactions are of primordial importance to the cell, and the structure of such interaction provides an important starting point for their further characterization. In many cases, the structure of the peptide-protein complex has not been solved by experiment, and modeling tools need to be applied to generate structural models of the interaction. PeptiMap is a protocol that identifies the peptide-binding site when only the structure of the receptor is known, but no information about where the peptide binds is available. This is achieved by mapping the surface for solvents to identify ligand-binding sites, similar in approach to ANCHORMAP in which amino acids are mapped. Peptimap is a free open access web-based server. It can be accessed at http://peptimap.cluspro.org.

Key words

Peptide-protein interactions Binding site prediction Solvent mapping Peptide mapping 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Biomedical EngineeringBoston UniversityBostonUSA
  2. 2.Department of Applied Mathematics and StatisticsStony Brook UniversityNew YorkUSA
  3. 3.Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical SchoolThe Hebrew University of JerusalemJerusalemIsrael

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